SPM DTI toolbox
This is a toolbox for playing with DTI data, including data import and export in DICOM, SPM and FSL format, creating mask images, and diagnosing slice artfacts, such as the DtiSpikingArtefact. It automates many of the preprocessing steps in [DiffusionFdtNotes]
First, get a version of the code - for now use the development versions - as below.
Then, to convert some DICOM FSL data to FSL format, try this:
You should find, after following a few prompts, that you have, in your selected output directory, two new directories:
- spm_dti (containing the DICOM-NIFTI converted SPM files and diffusion directions)
- fdt (containing data ready for input into the FSL fdt tool)
Let me know of any problems, it's in early testing.
To install a development code copy on your system
You will need subversion, and three repositories, like this:
cd my_directory svn co http://imaging.mrc-cbu.cam.ac.uk/svn/cbudti/devel cbudti svn co http://imaging.mrc-cbu.cam.ac.uk/svn/utilities/devel utilities # And for testing svn co http://imaging.mrc-cbu.cam.ac.uk/svn/testing/devel testing
Put all three of cbudti, utilities and (optionally) testing on your matlab path
For example, to get a copy of the current state of the development code:
svn export http://imaging.mrc-cbu.cam.ac.uk/svn/cbudti/devel cbudti
(this results in a new cbudti directory containing the code. To use it, put it on your matlab path (addpath /your/directory/cbudti).
To check out a versioned copy for editing or reviewing changes:
svn co http://imaging.mrc-cbu.cam.ac.uk/svn/cbudti/devel cbudti
Then (if you have permission) edit some file.
svn commit -m 'A comment'
cd cbudti; svn update
to get the latest repository data into your working copy in the cbudti subdirectory.